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- PDB-4g6a: Structure of the Hepatitis C virus envelope glycoprotein E2 antig... -

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Basic information

Entry
Database: PDB / ID: 4g6a
TitleStructure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody AP33
Components
  • AP33 Heavy Chain
  • AP33 Light chain
  • E2 peptide
KeywordsIMMUNE SYSTEM / Immunoglobulin Fold
Function / homology
Function and homology information


host cell lipid droplet / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsKong, L. / Wilson, I.A. / Law, M.
CitationJournal: J.Virol. / Year: 2012
Title: Structure of Hepatitis C Virus Envelope Glycoprotein E2 Antigenic Site 412 to 423 in Complex with Antibody AP33.
Authors: Kong, L. / Giang, E. / Nieusma, T. / Robbins, J.B. / Deller, M.C. / Stanfield, R.L. / Wilson, I.A. / Law, M.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: E2 peptide
A: E2 peptide
C: AP33 Heavy Chain
D: AP33 Light chain
H: AP33 Heavy Chain
L: AP33 Light chain


Theoretical massNumber of molelcules
Total (without water)98,7406
Polymers98,7406
Non-polymers00
Water3,423190
1
B: E2 peptide
C: AP33 Heavy Chain
D: AP33 Light chain


Theoretical massNumber of molelcules
Total (without water)49,3703
Polymers49,3703
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-37 kcal/mol
Surface area19530 Å2
MethodPISA
2
A: E2 peptide
H: AP33 Heavy Chain
L: AP33 Light chain


Theoretical massNumber of molelcules
Total (without water)49,3703
Polymers49,3703
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-36 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.875, 191.804, 59.374
Angle α, β, γ (deg.)90.00, 111.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide E2 peptide


Mass: 1554.710 Da / Num. of mol.: 2 / Fragment: E2 peptide / Source method: obtained synthetically
Details: this sequence naturally occurs in Hepatitis C virus
Source: (synth.) Hepatitis C virus / References: UniProt: Q9YK84
#2: Antibody AP33 Heavy Chain


Mass: 24103.893 Da / Num. of mol.: 2 / Fragment: antibody Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo Sapiens (human)
#3: Antibody AP33 Light chain


Mass: 23711.229 Da / Num. of mol.: 2 / Fragment: antibody Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo Sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 17% (w/v) PEG 4000, 8.5% (v/v) 2-propanol, 15% (v/v) glycerol and 0.085 M Sodium HEPES, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→47.97 Å / Num. all: 29450 / Num. obs: 29450 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.54 Å / % possible all: 61.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DGV

4dgv


Resolution: 2.501→47.97 Å / SU ML: 0.65 / σ(F): 1.43 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 1502 5.11 %RANDOM
Rwork0.178 ---
all0.1803 ---
obs0.1803 29409 91.27 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.244 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8749 Å2-0 Å2-11.0178 Å2
2---0.4665 Å2-0 Å2
3----3.4084 Å2
Refinement stepCycle: LAST / Resolution: 2.501→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6873 0 0 190 7063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037053
X-RAY DIFFRACTIONf_angle_d0.7869604
X-RAY DIFFRACTIONf_dihedral_angle_d12.1272504
X-RAY DIFFRACTIONf_chiral_restr0.0541101
X-RAY DIFFRACTIONf_plane_restr0.0041222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5009-2.58160.3202890.23321718X-RAY DIFFRACTION62
2.5816-2.67380.26591110.21511912X-RAY DIFFRACTION70
2.6738-2.78090.29411250.22062315X-RAY DIFFRACTION84
2.7809-2.90740.31321330.2092695X-RAY DIFFRACTION97
2.9074-3.06070.29141300.20652787X-RAY DIFFRACTION99
3.0607-3.25240.24291270.18672789X-RAY DIFFRACTION99
3.2524-3.50350.22641300.17252762X-RAY DIFFRACTION98
3.5035-3.85590.19371610.16312711X-RAY DIFFRACTION99
3.8559-4.41350.18441640.15622735X-RAY DIFFRACTION98
4.4135-5.55920.17861600.14422742X-RAY DIFFRACTION99
5.5592-47.9810.2081720.19142741X-RAY DIFFRACTION98

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